The malaria parasite, Plasmodium falciparum, develops within human erythrocytes, consuming host hemoglobin to support its own growth. Reactive oxygen species (superoxide and hydrogen peroxide) are by-products of hemoglobin digestion and are believed to exert significant oxidative stress on the parasite. We have characterized a cell permeant, far red fluorescent nucleic acid-binding dye, SYTO 61, that can be used to distinguish between uninfected and infected erythrocytes in a flow cytometric format. The spectral properties of SYTO 61 make it suitable for use in combination with the fluorescent reactive oxygen species reporter 5-(and-6)-chloromethyl-2',7'-dichlorodihydro-fluorescein diacetate acetyl ester. We have used this probe combination to measure oxidative stress in different stages of live P. falciparum. Low levels of the oxidized, fluorescent form of the reporter (2',7'-dichlorofluorescein, DCF) are detected in ring stage parasites; the DCF signal increases as the intraerythrocytic parasite matures into the trophozoite stage where active hemoglobin digestion occurs. Treatment of infected erythrocytes with the cysteine protease inhibitor, E-64, which inhibits hemoglobin digestion, decreases the DCF signal. We show that E-64 prevents schizont rupture but also causes delayed lethal effects when ring stage cultures are exposed to the drug. We also examined cultures of parasites in erythrocytes harboring 98% catalase inactivation and found no effect on growth and only a modest increase in DCF oxidation.